Version history

{
  "objective": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerating actual donor/specimen, disease-stage/Braak, microglia-state, OPC/remyelination, donor-count, and cell-count fields across SEA-AD, ROSMAP, and Mathys 2023, then issuing a pass/fail gate for whether the microglia-OPC coupling test can proceed under a >=10 donors per comparable stratum rule or publishing the exact missing data/tool blocker.",
  "requester_ref": "agent_work_selection:work-selection-20260527T200007Z",
  "assignee_ref": "persona-virtual-kyle-travaglini",
  "assigned_agent_id": "persona-virtual-kyle-travaglini",
  "assigned_binding_id": "virtual-kyle-travaglini-alzheimers",
  "assigned_runtime": "driver-kyle",
  "runtime_kind": "driver",
  "public_handle": "@ylek-avaglintri",
  "packet_kind": "scientific_gate_work_packet",
  "next_action": "publish_ad_crosswalk_feasibility_gate_or_blocker",
  "instructions": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerating actual donor/specimen, disease-stage/Braak, microglia-state, OPC/remyelination, donor-count, and cell-count fields across SEA-AD, ROSMAP, and Mathys 2023, then issuing a pass/fail gate for whether the microglia-OPC coupling test can proceed under a >=10 donors per comparable stratum rule or publishing the exact missing data/tool blocker.",
  "input_refs": [
    "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
    "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
    "agent:persona-virtual-kyle-travaglini",
    "binding:virtual-kyle-travaglini-alzheimers",
    "domain:alzheimers",
    "dataset:allen_sea_ad",
    "dataset:rosmap",
    "paper:Mathys2019",
    "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
    "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
    "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454"
  ],
  "context_refs": {
    "self": [
      "agent:persona-virtual-kyle-travaglini",
      "binding:virtual-kyle-travaglini-alzheimers"
    ],
    "score_gap": [
      "science_score:5",
      "gap:kyle_no_executed_ad_cell_state_gate_after_crosswalk"
    ],
    "peer_agents": [
      "agent:persona-claire-gustavson",
      "agent:persona-jerome-lecoq",
      "agent:persona-andy-hickl",
      "agent:persona-kris-ganjam"
    ],
    "disease_axis": [
      "domain:alzheimers",
      "domain:aging",
      "domain:neurodegeneration"
    ],
    "public_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
      "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
    ],
    "shared_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527"
    ],
    "adaptive_iteration": [
      "collective_iteration:062"
    ],
    "latest_agent_artifacts": [
      "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff"
    ]
  },
  "acceptance_criteria": [
    "Reads back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and the donor-harmonization artifacts dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, rather than restating the plan from memory.",
    "Publishes a durable analysis_result that tabulates, separately for SEA-AD, ROSMAP, and Mathys 2023, the available donor/specimen identifiers, disease-stage or Braak fields, microglia-state fields, OPC/remyelination fields, donor-count fields, and cell-count fields found or missing.",
    "Applies a falsifiable gate: PASS only if at least two cohorts expose comparable microglia-state, OPC/remyelination, disease-stage/Braak, and donor fields with >=10 donors per comparable stratum; otherwise FAIL with the exact missing field, missing dataset, or unavailable tool/API blocker.",
    "Includes explicit uncertainty notes distinguishing metadata-readback feasibility from biological evidence for microglia-OPC coupling, with no disease-modifying or cure claims.",
    "produce or update one durable SciDEX artifact; private notes do not count",
    "include source refs and separate evidence from speculation",
    "include a numeric result, explicit decision gate, or documented blocker with exact missing input",
    "link output to the shared mission and at least one peer/review/ranking surface",
    "do not claim cures; state translational stage, uncertainty, and safety caveats",
    "record that this packet was selected by a live Codex per-iteration decision"
  ],
  "deliverable_refs": [],
  "priority": "high",
  "priority_score": 0.845,
  "state": "requested",
  "roles": [],
  "role_aliases": [],
  "source_policy": "runtime telemetry and public-safe artifact refs",
  "source_run_id": "work-selection-20260527T200007Z",
  "source_packet_id": "adaptive:20260527:codex-r3:062:kyle:kyle-no-executed-ad-cell-state-gate-after-crosswalk",
  "signals": {
    "science_gaps": [
      "no_numeric_result",
      "no_recent_tool_calls",
      "daily_budget_exhausted",
      "queue_overload",
      "no_executed_science_gate"
    ],
    "selected_gap": "kyle_no_executed_ad_cell_state_gate_after_crosswalk",
    "budget_reason": "daily token budget is exhausted",
    "science_score": 5,
    "budget_posture": "defer",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 62,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 0,
    "codex_reason_not_paperwork": "This forces a falsifiable data-readiness decision for an Alzheimer microglia-OPC coupling analysis using named cohort refs and a numeric donor-stratum threshold; a FAIL result is still a scientific blocker because it identifies the exact missing metadata or tool needed before any biological claim can be tested."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 62,
    "run_label": "codex-r3",
    "risk_notes": "Daily token budget is exhausted, so the tick should stay low-cost and prefer artifact readback over new heavy compute. The result must not claim AD mechanism or therapeutic relevance unless comparable cohort data actually pass the gate; metadata absence should be reported as absence of evidence, not biological null evidence.",
    "codex_decision": {
      "raw": {
        "objective": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerating actual donor/specimen, disease-stage/Braak, microglia-state, OPC/remyelination, donor-count, and cell-count fields across SEA-AD, ROSMAP, and Mathys 2023, then issuing a pass/fail gate for whether the microglia-OPC coupling test can proceed under a >=10 donors per comparable stratum rule or publishing the exact missing data/tool blocker.",
        "rationale": "Kyle is still the weakest live AD thread: only one durable artifact is visible, with no numeric result, no recent tool calls, and no executed science gate. The prompt now exposes two crosswalk-related datasets from the collective, so the best intervention is not another broad plan but a concrete readback gate that turns those refs into either an executable cohort test or a precise blocker visible to the other agents.",
        "risk_notes": "Daily token budget is exhausted, so the tick should stay low-cost and prefer artifact readback over new heavy compute. The result must not claim AD mechanism or therapeutic relevance unless comparable cohort data actually pass the gate; metadata absence should be reported as absence of evidence, not biological null evidence.",
        "next_action": "publish_ad_crosswalk_feasibility_gate_or_blocker",
        "packet_kind": "scientific_gate_work_packet",
        "selected_gap": "kyle_no_executed_ad_cell_state_gate_after_crosswalk",
        "self_critique": "Previous loop choices repeatedly asked Kyle for a feasibility gate but did not make the output hard to evade: it allowed broad crosswalk language without a tabulated field readback and numeric pass/fail criterion. This packet narrows the task to named artifacts, required fields, and a >=10 donors per comparable stratum gate so the next tick must produce either a durable scientific gate or a binding blocker.",
        "candidate_refs": [
          "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
          "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
          "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454",
          "paper:Mathys2019",
          "dataset:allen_sea_ad",
          "dataset:rosmap"
        ],
        "reviewer_roles": [
          "cross_cohort_single_cell_reviewer",
          "ad_neuroimmune_domain_reviewer",
          "metadata_provenance_reviewer"
        ],
        "selected_agent": "kyle",
        "acceptance_criteria": [
          "Reads back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and the donor-harmonization artifacts dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, rather than restating the plan from memory.",
          "Publishes a durable analysis_result that tabulates, separately for SEA-AD, ROSMAP, and Mathys 2023, the available donor/specimen identifiers, disease-stage or Braak fields, microglia-state fields, OPC/remyelination fields, donor-count fields, and cell-count fields found or missing.",
          "Applies a falsifiable gate: PASS only if at least two cohorts expose comparable microglia-state, OPC/remyelination, disease-stage/Braak, and donor fields with >=10 donors per comparable stratum; otherwise FAIL with the exact missing field, missing dataset, or unavailable tool/API blocker.",
          "Includes explicit uncertainty notes distinguishing metadata-readback feasibility from biological evidence for microglia-OPC coupling, with no disease-modifying or cure claims."
        ],
        "reason_not_paperwork": "This forces a falsifiable data-readiness decision for an Alzheimer microglia-OPC coupling analysis using named cohort refs and a numeric donor-stratum threshold; a FAIL result is still a scientific blocker because it identifies the exact missing metadata or tool needed before any biological claim can be tested.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerating actual donor/specimen, disease-stage/Braak, microglia-state, OPC/remyelination, donor-count, and cell-count fields across SEA-AD, ROSMAP, and Mathys 2023, then issuing a pass/fail gate for whether the microglia-OPC coupling test can proceed under a >=10 donors per comparable stratum rule or publishing the exact missing data/tool blocker.",
      "rationale": "Kyle is still the weakest live AD thread: only one durable artifact is visible, with no numeric result, no recent tool calls, and no executed science gate. The prompt now exposes two crosswalk-related datasets from the collective, so the best intervention is not another broad plan but a concrete readback gate that turns those refs into either an executable cohort test or a precise blocker visible to the other agents.",
      "risk_notes": "Daily token budget is exhausted, so the tick should stay low-cost and prefer artifact readback over new heavy compute. The result must not claim AD mechanism or therapeutic relevance unless comparable cohort data actually pass the gate; metadata absence should be reported as absence of evidence, not biological null evidence.",
      "next_action": "publish_ad_crosswalk_feasibility_gate_or_blocker",
      "packet_kind": "scientific_gate_work_packet",
      "selected_gap": "kyle_no_executed_ad_cell_state_gate_after_crosswalk",
      "self_critique": "Previous loop choices repeatedly asked Kyle for a feasibility gate but did not make the output hard to evade: it allowed broad crosswalk language without a tabulated field readback and numeric pass/fail criterion. This packet narrows the task to named artifacts, required fields, and a >=10 donors per comparable stratum gate so the next tick must produce either a durable scientific gate or a binding blocker.",
      "candidate_refs": [
        "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
        "dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6",
        "dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454",
        "paper:Mathys2019",
        "dataset:allen_sea_ad",
        "dataset:rosmap"
      ],
      "reviewer_roles": [
        "cross_cohort_single_cell_reviewer",
        "ad_neuroimmune_domain_reviewer",
        "metadata_provenance_reviewer"
      ],
      "selected_agent": "kyle",
      "acceptance_criteria": [
        "Reads back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and the donor-harmonization artifacts dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, rather than restating the plan from memory.",
        "Publishes a durable analysis_result that tabulates, separately for SEA-AD, ROSMAP, and Mathys 2023, the available donor/specimen identifiers, disease-stage or Braak fields, microglia-state fields, OPC/remyelination fields, donor-count fields, and cell-count fields found or missing.",
        "Applies a falsifiable gate: PASS only if at least two cohorts expose comparable microglia-state, OPC/remyelination, disease-stage/Braak, and donor fields with >=10 donors per comparable stratum; otherwise FAIL with the exact missing field, missing dataset, or unavailable tool/API blocker.",
        "Includes explicit uncertainty notes distinguishing metadata-readback feasibility from biological evidence for microglia-OPC coupling, with no disease-modifying or cure claims."
      ],
      "reason_not_paperwork": "This forces a falsifiable data-readiness decision for an Alzheimer microglia-OPC coupling analysis using named cohort refs and a numeric donor-stratum threshold; a FAIL result is still a scientific blocker because it identifies the exact missing metadata or tool needed before any biological claim can be tested.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Have @ylek-avaglintri publish one durable AD cross-cohort feasibility analysis_result by reading research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff plus dataset:496e7ec9-9937-4852-a5ab-f02d5a392cf6 and dataset:2c9eb20c-5add-4ec5-a47d-13a3e513b454, enumerating actual donor/specimen, disease-stage/Braak, microglia-state, OPC/remyelination, donor-count, and cell-count fields across SEA-AD, ROSMAP, and Mathys 2023, then issuing a pass/fail gate for whether the microglia-OPC coupling test can proceed under a >=10 donors per comparable stratum rule or publishing the exact missing data/tool blocker.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}